search

mskcc / cwl-commandlinetools

Central location for CWL CommandLineTools
Other
3 stars 3 forks source link

merge msk-access tools #86

Closed ionox0 closed 3 years ago

ionox0 commented 3 years ago

Hoping to merge the msk-access Fork of this repo back into MSKCC fork so that we can use the merge_fastq tool in Beagle

The changes include deleting the workflows directory (as this is a repo for just commandlinetools), and adding several tools being used by the ACCESS team.

ionox0 commented 3 years ago

@rhshah

Currently Ridgeback will look for the term "access" inside of the pipeline URL to decide whether to use our ACCESS toil-cwl-runner command, or the default ridgeback toil command (without --no-container).

Since we need containers to run the merge_fastq tool, that means we need to use the ridgeback toil command, and thus we can't have the word "access" in the pipeline URL.

If you can merge this for us we will be able to run the merge_fastq tool from this fork, and it will run with the default ridgeback toil command.

ionox0 commented 3 years ago

However, this is all based on the premise that the CI team is ok with us making all of these changes to this repo (I was under the impression that it is no longer in use by CI team).

Please let us know @allanbolipata @sivkovic @nikhil if you would prefer us to do this a different way.